Campaign 2016 (PhD Chapter 1)


This series of files compile all analyses done during Chapter 1 for the regional campaign of 2016.

All analyses have been done with PRIMER-e 6 and R 3.6.0.

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Caracteristics of each campaign

2014 2016 2017
Sampling date August-September June to August July
Criteria for perturbation Potentially impacted if close to the city or industries, References outside the bay Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria
Regions considered BSI BSI, CPC, BDA, MR BSI, MR
Number of sampled stations 40 (20 HI, 20 R) 78 (26 BSI, 19 CPC, 18 BDA, 15 MR) 126 (111 BSI, 15 MR)
Parameters sampled Organic matter yes yes yes
Photosynthetic pigments no yes yes
Sediment grain-size yes yes yes
Heavy-metals yes yes (for a limited number of stations) no (interpolated based on 2014 and 2016 values)
Benthic communities Compartment targeted Macro-infauna Macro-infauna Macro-infauna
Sieved used 500 µm 1 mm 500 µm and 1 mm
Conservation technique Formaldehyle Formaldehyle Formaldehyle
Others N.A. N.A. N.A.

We used data from subtidal ecosystems (see metadata files for more information). Only stations that have been sampled both for abiotic parameters and benthic species were included.

Selected variables for the analyses:

Abundances of Mesodesma arctatum (Marc) and Cistenides granulata (Cgra) were also considered (see IndVal and SIMPER results).

As data is missing for metal concentrations outside BSI, two Designs have been used:

Statistics for each variable considered:

BSI, CPC, BDA, MR (without heavy metals)
  Mean SD SE Median Min Max 95% CI
depth 20.362 16.975 1.947 15.500 1.000 65.900 3.816
om 0.691 0.738 0.085 0.384 0.168 3.863 0.166
gravel 0.046 0.118 0.014 0.000 0.000 0.809 0.027
sand 0.707 0.352 0.040 0.883 0.000 1.001 0.079
silt 0.203 0.288 0.033 0.031 0.000 0.942 0.065
clay 0.044 0.099 0.011 0.006 0.000 0.497 0.022
S 4.671 2.895 0.332 4.000 0.000 13.000 0.651
N 19.408 25.758 2.955 12.000 0.000 142.000 5.791
H 1.059 0.603 0.069 1.025 0.000 2.307 0.136
J 0.721 0.295 0.034 0.838 0.000 1.000 0.066
BSI (only heavy metals)
  Mean SD SE Median Min Max 95% CI
arsenic 4.300 4.759 0.971 2.500 0.800 21.300 1.904
cadmium 0.153 0.048 0.010 0.145 0.080 0.270 0.019
chromium 49.667 24.539 5.009 40.500 17.000 111.000 9.817
copper 9.787 7.764 1.585 7.800 2.400 28.800 3.106
iron 45356.633 17343.813 3540.291 39733.450 21938.100 85408.600 6938.843
manganese 776.663 362.884 74.073 677.850 318.400 1657.100 145.181
mercury 0.023 0.017 0.004 0.019 0.007 0.091 0.007
lead 5.421 3.021 0.617 4.650 1.900 12.200 1.209
zinc 59.358 30.340 6.193 47.700 26.900 141.400 12.138

1. Maps

1.1. General map

1.2. Parameters maps

For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity (grey = low toxicity, red = high toxicity).

OM

Gravel

Sand

Silt

Clay

Arsenic

Cadmium

Chromium

Copper

Iron

Manganese

Mercury

Lead

Zinc

Species

Total abundance

Shannon index

Piélou’s evenness

2. Figures

2.1. Barplots

Two types of barplots are available: one for the means by region, and one for the means by depth class. The latter have been done by classifying stations along three groups, based on their depth: shallow (0-10 m), medium (10-25 m) and deep (> 25 m). These thresholds are not supported by evidence, but allow to get a balanced design (26 stations for each depth class). However, we have been using PERMANOVA with depth as a covariate, instead of using these classes as a third factor.

Heavy metals are not presented here, as they were only sampled at BSI stations.

Regions

Organic matter

Grain-size

Species abundances

Diversity indices

Depth classes

Organic matter

Grain-size

Species abundances

Diversity indices

2.2. Phylum frequencies

Conditions

Phylum abundances by condition
Phylum HI R
Annelida 275 231
Echinodermata 230 162
Mollusca 196 189
Arthropoda 110 73
Platyhelminthes 3 0
Nematoda 1 0
Nemertea 1 0
Brachiopoda 0 2
Cnidaria 0 2

Regions

Phylum abundances by region
Phylum BSI CPC BDA MR
Annelida 206 69 188 43
Mollusca 151 45 89 100
Arthropoda 97 13 30 43
Echinodermata 24 206 24 138
Platyhelminthes 3 0 0 0
Nematoda 1 0 0 0
Nemertea 1 0 0 0
Brachiopoda 0 0 0 2
Cnidaria 0 0 0 2

2.3. Species estimation curves

2.4. Principal Component Analysis

Design 1

Variables have been scaled by mean and standard-deviation prior to analysis.

Design 2

Variables have been scaled by mean and standard-deviation prior to analysis.

2.5. Non-metric Multidimensional Scaling

Design 1

Variables have been scaled by mean and standard-deviation prior to analysis.

Design 2

Variables have been scaled by mean and standard-deviation prior to analysis.

Species

Stations with no species were deleted from this analysis.

2.6. Hierarchical Agglomerative Clustering

Design 1

Variables have been scaled by mean and standard-deviation prior to analysis.

##  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75 
##   1   2   2   2   2   2   2   2   2   2   3   3   2   3   2   1   3   2   2   2   2   2   2   2   2   2   2   1   1   1   1   2 
##  76  77  78  79  80  82  83  86  87  88  90  92  93  94  95  96  97  98  99 100 101 102 103 104 105 106 107 108 109 110 111 112 
##   1   2   2   2   3   3   3   2   2   2   3   1   3   2   1   3   1   3   1   1   3   2   3   3   1   2   1   3   2   1   3   1 
## 113 114 115 116 117 118 119 120 121 122 123 124 
##   2   2   2   3   3   3   2   2   1   2   3   3

Design 2

Variables have been scaled by mean and standard-deviation prior to analysis.

## 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 
##   1   2   1   1   3   3   3   1   3   3   3   3   3   3   3   2   2   2   2   3   3   3   3   2

Species

Stations with no species were deleted from this analysis.

##  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75 
##   1   1   1   1   1   1   1   1   1   2   1   1   3   1   2   2   1   2   2   2   1   1   1   1   3   1   2   2   1   1   2   2 
##  76  77  78  79  82  83  86  87  90  92  93  94  95  96  97  98  99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 
##   1   1   2   2   1   3   1   2   1   2   3   3   1   1   3   1   3   3   1   1   1   1   1   1   1   1   1   1   1   3   1   3 
## 115 116 117 118 119 120 121 122 123 124 
##   1   1   1   1   1   2   1   3   1   1


Elliot Dreujou

2020-01-24